.. _scil_bundle_compute_endpoints_map:

scil_bundle_compute_endpoints_map
=================================

::

	usage: __main__.py [-h] [--out_json OUT_JSON] [--swap] [--binary]
	                   [--distance DISTANCE] [--unit {points,mm}]
	                   [--indent INDENT] [--sort_keys] [--reference REFERENCE]
	                   [-v [{DEBUG,INFO,WARNING,ERROR}]] [-f]
	                   in_bundle endpoints_map_head endpoints_map_tail
	
	Computes the endpoints maps of a bundle (head and tail). The endpoints maps are
	a count of the number of streamlines that start or end in each voxel.
	
	Note: If the streamlines are not ordered, the head/tail are random and not
	really two coherent groups.
	    - To get a single endpoint map of all endpoints, without grouping the head
	    and tail, use
	        >> scil_tractogram_compute_density_map --endpoints_only
	    - To order streamlines so that they start and end in the same regions, use
	        >> scil_bundle_uniformize_endpoints
	
	positional arguments:
	  in_bundle             Fiber bundle filename.
	  endpoints_map_head    Output endpoints map head filename.
	  endpoints_map_tail    Output endpoints map tail filename.
	
	options:
	  -h, --help            show this help message and exit
	  --out_json OUT_JSON   Output JSON file with the number of streamlines in each endpoint map. [endpoints_map.json]
	  --swap                Swap head<->tail convention. Can be useful when the reference is not in RAS.
	  --binary              Save outputs as a binary mask instead of a heat map.
	  --reference REFERENCE
	                        Reference anatomy for tck/vtk/fib/dpy file
	                        support (.nii or .nii.gz).
	  -v [{DEBUG,INFO,WARNING,ERROR}]
	                        Produces verbose output depending on the provided level. 
	                        Default level is warning, default when using -v is info.
	  -f                    Force overwriting of the output files.
	
	Distance options:
	  --distance DISTANCE   Distance to consider at the extremities of the streamlines. 
	                        Ex: if --unit is points, a value of 1 means that the first and last 
	                        points of the streamlines only are considered.[1]
	  --unit {points,mm}    Unit of the distance. [points]
	
	Json options:
	  --indent INDENT       Indent for json pretty print.
	  --sort_keys           Sort keys in output json.
	
	2.2.2